In this project we use next generation sequencing approaches to sequence the adaptive immune receptors of antigen-specific B cells and T cells. The sequencing is increasingly at the single cell level and paired with whole transcriptome analysis. We do this in the context of vaccination, natural infection and mouse models of cancer. The aim is to understand the nature of effective antigen-specific adaptive immune responses. We have implemented the two 10x Genomic Chromium platforms purchased 6 months ago and we are currently using these to massively increase our throughput of single cell 5 and 3 transcriptome sequencing. We have successfully developed and implemented a custom primer library prep approach so that we may adapt the standard 10x 5 immunoglobulin and T cell receptor sequencing protocol for use with samples from rhesus and cynomolgus macaques, and Guinea pigs. In addition, we have increased the sensitivity of the library prep by 100-fold by removing the fragmentation step. We have implemented CITE-seq applications using custom conjugated antibodies to perform high parameter cell surface proteomics. All of these approaches have been used to investigate the nature and evolution of antigen-specific T cell and antibody responses in HIV, cancer, and influenza as outlined in the list of publications.